ORF8 and ORF3b antibodies are accurate serological markers of early and late SARS-CoV-2 infection.

The SARS-CoV-2 virus emerged in December 2019 and has caused a worldwide pandemic due to the lack of any pre-existing immunity. Accurate serology testing is urgently needed to help diagnose infection, determine past exposure of populations and assess the response to a future vaccine. The landscape of antibody responses to SARS-CoV-2 is unknown. In this study, we utilized the luciferase immunoprecipitation system to assess the antibody responses to 15 different SARS-CoV-2 antigens in patients with COVID-19. We identified new targets of the immune response to SARS-CoV-2 and show that nucleocapsid, open reading frame (ORF)8 and ORF3b elicit the strongest specific antibody responses. ORF8 and ORF3b antibodies, taken together as a cluster of points, identified 96.5% of COVID-19 samples at early and late time points of disease with 99.5% specificity. Our findings could be used to develop second-generation diagnostic tests to improve serological assays for COVID-19 and are important in understanding pathogenicity.

Author Correction: ORF8 and ORF3b antibodies are accurate serological markers of early and late SARS-CoV-2 infection.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Pathogenesis and transmission of SARS-CoV-2 in golden hamsters.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus with high nucleotide identity to SARS-CoV and to SARS-related coronaviruses that have been detected in horseshoe bats, has spread across the world and had a global effect on healthcare systems and economies1,2. A suitable small animal model is needed to support the development of vaccines and therapies. Here we report the pathogenesis and transmissibility of SARS-CoV-2 in golden (Syrian) hamsters (Mesocricetus auratus). Immunohistochemistry assay demonstrated the presence of viral antigens in nasal mucosa, bronchial epithelial cells and areas of lung consolidation on days 2 and 5 after inoculation with SARS-CoV-2, followed by rapid viral clearance and pneumocyte hyperplasia at 7 days after inoculation. We also found viral antigens in epithelial cells of the duodenum, and detected viral RNA in faeces. Notably, SARS-CoV-2 was transmitted efficiently from inoculated hamsters to naive hamsters by direct contact and via aerosols. Transmission via fomites in soiled cages was not as efficient. Although viral RNA was continuously detected in the nasal washes of inoculated hamsters for 14 days, the communicable period was short and correlated with the detection of infectious virus but not viral RNA. Inoculated and naturally infected hamsters showed apparent weight loss on days 6-7 post-inoculation or post-contact; all hamsters returned to their original weight within 14 days and developed neutralizing antibodies. Our results suggest that features associated with SARS-CoV-2 infection in golden hamsters resemble those found in humans with mild SARS-CoV-2 infections.

Avian Influenza A(H5N1) Neuraminidase Inhibition Antibodies in Healthy Adults after Exposure to Influenza A(H1N1)pdm09.

We detected high titers of cross-reactive neuraminidase inhibition antibodies to influenza A(H5N1) virus clade 2.3.4.4b in 96.8% (61/63) of serum samples from healthy adults in Hong Kong in 2020. In contrast, antibodies at low titers were detected in 42% (21/50) of serum samples collected in 2009. Influenza A(H1N1)pdm09 and A(H5N1) titers were correlated.

Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong.

Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.

Managing temperature in open quantum systems strongly coupled with structured environments.

In non-perturbative non-Markovian open quantum systems, reaching either low temperatures with the hierarchical equations of motion (HEOM) or high temperatures with the Thermalized Time Evolving Density Operator with Orthogonal Polynomials Algorithm (T-TEDOPA) formalism in Hilbert space remains challenging. We compare different ways of modeling the environment. Sampling the Fourier transform of the bath correlation function, also called temperature dependent spectral density, proves to be very effective. T-TEDOPA [Tamascelli et al., Phys. Rev. Lett. 123, 090402 (2019)] uses a linear chain of oscillators with positive and negative frequencies, while HEOM is based on the complex poles of an optimized rational decomposition of the temperature dependent spectral density [Xu et al., Phys. Rev. Lett. 129, 230601 (2022)]. Resorting to the poles of the temperature independent spectral density and of the Bose function separately is an alternative when the problem due to the huge number of Bose poles at low temperatures is circumvented. Two examples illustrate the effectiveness of the HEOM and T-TEDOPA approaches: a benchmark pure dephasing case and a two-bath model simulating the dynamics of excited electronic states coupled through a conical intersection. We show the efficiency of T-TEDOPA to simulate dynamics at a finite temperature by using either continuous spectral densities or only all the intramolecular oscillators of a linear vibronic model calibrated from ab initio data of a phenylene ethynylene dimer.

A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase.

During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.

Identification of urgent gaps in public and policymaker knowledge of heart failure: Results of a global survey.

BACKGROUND: Despite advances in the treatment of heart failure (HF) with reduced ejection fraction, people with HF continue to have a high risk of mortality and hospitalisation. Patients also suffer from poor quality of life, with reduced societal and economic participation. The burden of HF on patients and healthcare systems is extraordinary, yet awareness remains low. This survey was conducted to identify gaps in general public and policymaker knowledge around HF. METHODS: A closed-question web-based survey of the general public and policymakers was conducted between February and October 2020. Study outcomes assessed the participants' awareness and understanding of HF symptoms, risk factors and mortality, and views around hospital admissions in their country. Responses were collected using multiple-choice questions. RESULTS: The survey was completed by 26,272 general public respondents in 13 countries and 281 government and public sector policymakers in nine countries. While 99% of general public respondents had heard of HF, their understanding of the condition and its symptoms was poor, and only 6% identified that shortness of breath, fatigue, and leg swelling were the main symptoms of HF. Of policymaker respondents, 14% identified HF as the leading cause of avoidable hospitalisations, and only 4% recognised that ~ 87% of government spending on HF is related to hospitalisations. CONCLUSIONS: Major gaps were identified in the understanding of HF and the burden it places on patients and their caregivers, healthcare systems and society. This study confirms an ongoing need for national policy strategies and investment to raise awareness of the importance of HF prevention, early diagnosis, and implementation of effective treatments to reduce hospitalisations and death.

Increased Stability of SARS-CoV-2 Omicron Variant over Ancestral Strain.

As of April 2022, the Omicron BA.1 variant of concern of SARS-CoV-2 was spreading quickly around the world and outcompeting other circulating strains. We examined its stability on various surfaces and found that this Omicron variant is more stable than its ancestral strain on smooth and porous surfaces.

Apparent failed and discordant adrenal vein sampling: A potential confounding role of cortisol cosecretion?

OBJECTIVE: Adrenal vein sampling (AVS) and computed tomography (CT) often show confusingly discordant lateralisation results in primary aldosteronism (PA). We tested a biochemical algorithm using AVS data to detect cortisol cosecretion as a potential explanation for discordant cases. DESIGN: Retrospective analysis from a large PA + AVS database. PATIENTS: All patients with PA and AVS, 2005-2020. MEASUREMENTS: An algorithm using biochemical data from paired AVS + CT images was devised from physiological first principles and informed by data from unilateral, AVS-CT concordant patients. The algorithm involved calculations based upon the expectation that low cortisol levels exist in adrenal vein effluent opposite an aldosterone-and-cortisol-producing adrenal mass and may reverse lateralisation due to inflated aldosterone/cortisol ratios. MAIN OUTCOMES: The algorithm was applied to cases with discordant CT-AVS lateralisation to determine whether this might be a common or explanatory finding. Clinical and biochemical characteristics of identified cases were collected via chart review and compared to CT-AVS concordant cases to detect evidence of biological plausibility for cortisol cosecretion. RESULTS: From a total of 588 AVS cases, 141 AVS + CT pairs were clear unilateral PA cases, used to develop the three-step algorithm for AVS interpretation. Applied to 88 AVS + CT discordant pairs, the algorithm suggested possible cortisol cosecretion in 40%. Case review showed that the proposed cortisol cosecretors, as identified by the algorithm, had low/suppressed adrenocorticotropic hormone levels, larger average nodule size and lower plasma aldosterone. CONCLUSIONS: Pending external validation and outcome verification by surgery and tissue immunohistochemistry, cortisol cosecretion from aldosteronomas may be a common explanation for discordant CT-AVS results in PA.

Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests.

Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per µL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2-10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.

Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue.

Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute-solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute-solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.

Matrix Product State Simulations of Non-Equilibrium Steady States and Transient Heat Flows in the Two-Bath Spin-Boson Model at Finite Temperatures.

Simulating the non-perturbative and non-Markovian dynamics of open quantum systems is a very challenging many body problem, due to the need to evolve both the system and its environments on an equal footing. Tensor network and matrix product states (MPS) have emerged as powerful tools for open system models, but the numerical resources required to treat finite-temperature environments grow extremely rapidly and limit their applications. In this study we use time-dependent variational evolution of MPS to explore the striking theory of Tamascelli et al. (Phys. Rev. Lett. 2019, 123, 090402.) that shows how finite-temperature open dynamics can be obtained from zero temperature, i.e., pure wave function, simulations. Using this approach, we produce a benchmark dataset for the dynamics of the Ohmic spin-boson model across a wide range of coupling strengths and temperatures, and also present a detailed analysis of the numerical costs of simulating non-equilibrium steady states, such as those emerging from the non-perturbative coupling of a qubit to baths at different temperatures. Despite ever-growing resource requirements, we find that converged non-perturbative results can be obtained, and we discuss a number of recent ideas and numerical techniques that should allow wide application of MPS to complex open quantum systems.

SARS-CoV-2 Virus Culture and Subgenomic RNA for Respiratory Specimens from Patients with Mild Coronavirus Disease.

We investigated 68 respiratory specimens from 35 coronavirus disease patients in Hong Kong, of whom 32 had mild disease. We found that severe acute respiratory syndrome coronavirus 2 and subgenomic RNA were rarely detectable beyond 8 days after onset of illness. However, virus RNA was detectable for many weeks by reverse transcription PCR.

Thyroid function testing and management during and after pregnancy among women without thyroid disease before pregnancy.

BACKGROUND: Screening in pregnancy for subclinical hypothyroidism, often defined as thyroid-stimulating hormone (TSH) greater than 2.5 mIU/L or greater than 4.0 mIU/L, is controversial. We determined the frequency and distribution of TSH testing by gestational age, as well as TSH values associated with treatment during pregnancy and the frequency of postpartum continuation of thyroid hormone therapy. METHODS: We performed a retrospective cohort study of pregnancies in Alberta, Canada. We included women without thyroid disease who delivered between October 2014 and September 2017. We used delivery records, physician billings, and pharmacy and laboratory administrative data. Our key outcomes were characteristics of TSH testing and the initiation and continuation of thyroid hormone therapy. We calculated the proportion of pregnancies with thyroid testing and the frequency of each specific thyroid test. RESULTS: Of the 188 490 pregnancies included, 111 522 (59.2%) had at least 1 TSH measurement. The most common time for testing was at gestational week 5 to 6. Thyroid hormone therapy was initiated at a median gestational age of 7 (interquartile range 5-12) weeks. Among women with first TSH measurements of 4.01 to 9.99 mIU/L who were not immediately treated, the repeat TSH measurement was 4.00 mIU/L or below in 67.9% of pregnancies. Thyroid hormone was continued post partum for 44.6% of the women who started therapy during their pregnancy. INTERPRETATION: The findings of our study suggest that current practice patterns may contribute to overdiagnosis of hypothyroidism and overtreatment during pregnancy and post partum.

Effect of moist heat reprocessing of N95 respirators on SARS-CoV-2 inactivation and respirator function.

BACKGROUND: Unprecedented demand for N95 respirators during the coronavirus disease 2019 (COVID-19) pandemic has led to a global shortage of these masks. We validated a rapidly applicable, low-cost decontamination protocol in compliance with regulatory standards to enable the safe reuse of N95 respirators. METHODS: We inoculated 4 common models of N95 respirators with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and evaluated viral inactivation after disinfection for 60 minutes at 70°C and 0% relative humidity. Similarly, we evaluated thermal disinfection at 0% to 70% relative humidity for masks inoculated with Escherichia coli. We assessed masks subjected to multiple cycles of thermal disinfection for structural integrity using scanning electron microscopy and for protective functions using standards of the United States National Institute for Occupational Safety and Health for particle filtration efficiency, breathing resistance and respirator fit. RESULTS: A single heat treatment rendered SARS-CoV-2 undetectable in all mask samples. Compared with untreated inoculated control masks, E. coli cultures at 24 hours were virtually undetectable from masks treated at 70°C and 50% relative humidity (optical density at 600 nm wavelength, 0.02 ± 0.02 v. 2.77 ± 0.09, p < 0.001), but contamination persisted for masks treated at lower relative humidity. After 10 disinfection cycles, masks maintained fibre diameters similar to untreated masks and continued to meet standards for fit, filtration efficiency and breathing resistance. INTERPRETATION: Thermal disinfection successfully decontaminated N95 respirators without impairing structural integrity or function. This process could be used in hospitals and long-term care facilities with commonly available equipment to mitigate the depletion of N95 masks.

First principles modeling of exciton-polaritons in polydiacetylene chains.

Exciton-polaritons in organic materials are hybrid states that result from the strong interaction of photons and the bound excitons that these materials host. Organic polaritons hold great interest for optoelectronic applications; however, progress toward this end has been impeded by the lack of a first principles approach that quantifies light-matter interactions in these systems, which would allow the formulation of molecular design rules. Here, we present a theoretical framework that combines first principles calculations for excitons with classical electrodynamics in order to quantify light-matter interactions. We exemplify our approach by studying variants of the conjugated polymer polydiacetylene, and we show that a large polymer conjugation length is critical toward strong exciton-photon coupling, hence underlying the importance of pure structures without static disorder. By comparing to our experimental reflectivity measurements, we show that the coupling of excitons to vibrations, manifested by phonon side bands in the absorption, has a strong impact on the magnitude of light-matter coupling over a range of frequencies. Our approach opens the way toward a deeper understanding of polaritons in organic materials, and we highlight that a quantitatively accurate calculation of the exciton-photon interaction would require accounting for all sources of disorder self-consistently.

Switching between Coherent and Incoherent Singlet Fission via Solvent-Induced Symmetry Breaking.

Singlet fission in organic semiconductors causes a singlet exciton to decay into a pair of triplet excitons and holds potential for increasing the efficiency of photovoltaic devices. In this combined experimental and theoretical study, we reveal that a covalent dimer of the organic semiconductor tetracene undergoes activated singlet fission by qualitatively different mechanisms depending on the solvent environment. We show that intramolecular vibrations are an integral part of this mechanism, giving rise to mixing between charge transfer and triplet pair excitations. Either coherent or incoherent singlet fission can occur, depending on the transient solvent-induced energetic proximity between the states, giving rise to complex variation of the singlet fission mechanism and time scale in the different environments. Our results suggest a more general principle for controlling the efficiency of photochemical reactions by utilizing transient interactions to tune the energetics of reactant and product states and switch between incoherent and coherent dynamics.

Erratum: Tensor Network Simulation of Non-Markovian Dynamics in Organic Polaritons [Phys. Rev. Lett. 121, 227401 (2018)].

This corrects the article DOI: 10.1103/PhysRevLett.121.227401.

Prognostic Significance of P16 Expression and P53 Expression in Primary Vaginal Cancer.

To evaluate the correlation between p16 expression and clinical outcomes in patients with primary vaginal cancer treated with definitive radiotherapy. P16 immunohistochemical was performed on 25 patient samples and recorded from pathology reports in 7 patients. P53 immunohistochemical was performed on 3 p16-negative samples. Baseline characteristics were compared using the Fisher exact test. Outcomes were compared using log-rank tests, and cox proportional hazards models. Survival and recurrence analysis was performed with the Kaplan-Meier method and cumulative incidence estimates. P16 expression was positive in 29 patients and negative in 3 patients. Two of the p16-negative tumors showed positive expression of p53. The median overall survival, progression-free survival and 2-yr cumulative incidence of recurrence were 66 mo [95% confidence interval (CI), 31-96], 34 mo (95% CI, 21-86), and 19% (95% CI, 7%-34%), respectively. P16-positive tumors had higher median overall survival and progression-free survival compared with p16-negative tumors (82 vs. 31 mo, P=0.02 and 35 vs 16 mo, P=0.04, respectively). The 2-yr cumulative incidence of recurrence was 14% for p16-positive tumors compared with 67% for p16-negative tumors (P=0.07). On univariable analysis, p16-negative status, age older than 65, and advanced stage were associated with inferior overall survival. P16 negativity is an independent predictor of inferior overall survival. P16-positive vaginal cancers have a better prognosis and decreased incidence of recurrence compared with p16-negative tumors. These prognostic findings associated with p16-negative vaginal cancers will need to be confirmed in larger patient cohorts.